scholarly journals A57 An evolutionary framework to guide the hunt for human dsDNA viruses

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
A Aghebatrafat ◽  
K Merkel ◽  
F Leendertz ◽  
D H Krüger ◽  
S Calvignac-Spencer
Keyword(s):  
Phylogenetic Position ◽  
Second Phase ◽  
Dsdna Virus ◽  
Human Virus ◽  
Specific Pcr ◽  
Copy Numbers ◽  
History Of ◽  
Human Viruses ◽  
Next Generation Sequencing Ngs ◽  
Dsdna Viruses

Abstract It is becoming increasingly obvious that we only know a fraction of the human virome. The development of next-generation sequencing (NGS) technologies has dramatically increased our ability to hunt viruses. Yet, the small genomes and low copy numbers characteristic of most viruses make undirected (shotgun) hunts a relatively inefficient strategy. Here, we propose to speed-up the rate of double-stranded DNA (dsDNA) virus discovery by combining NGS with evolutionary thinking. dsDNA viruses are thought to have co-diverged with their hosts. As this applies to the hominine lineages (gorillas, humans, chimpanzees, and bonobos), it is theoretically possible to estimate the phylogenetic position of cryptic human viruses by identifying co-divergent viral lineages infecting non-human hominines. Where these lineages do not comprise a human-infecting counterpart, a yet-unknown human virus may be hiding. The first phase of this project will consist in the high-throughput characterization of dsDNA viruses (herpesviruses, papillomaviruses, and polyomaviruses) infecting wild gorillas, chimpanzees, and bonobos. For this, we will use an exhaustive collection of fecal samples (in terms of hominine species/sub-species diversity) and apply a discovery strategy combining in-solution capture and NGS. This strategy has been developed in the ancient DNA field but has a very broad applicability; it will constitute a nice addendum to the institute technical portfolio. Thanks to the massive amount of information collected, we will be able to reconstruct the evolutionary history of many dsDNA virus lineages and to identify those where a human virus would be expected but is still unknown. This will pave the way to the second phase of the project which will consist in a pre-oriented dsDNA human virus hunt based on the use of specific PCR systems implemented in multiplex. We expect that this project will generate an unprecedented amount of data on the processes at play along dsDNA virus evolution (co-divergence versus cross-species transmission), help determine the directionality, frequency, and timing of cross-species transmission events between hominines and unveil the existence of yet-to-be-discovered human viruses.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

Effects on insulin secretion and insulin action of a 48-h reduction of plasma free fatty acids with acipimox in nondiabetic subjects genetically predisposed to type 2 diabetes

2007 ◽  
Vol 292 (6) ◽  
pp. E1775-E1781 ◽  
Author(s):  
Kenneth Cusi ◽  
Sangeeta Kashyap ◽  
Amalia Gastaldelli ◽  
Mandeep Bajaj ◽  
Eugenio Cersosimo
Keyword(s):  
Type 2 Diabetes ◽  
Insulin Secretion ◽  
Family History ◽  
Second Phase ◽  
Β Cell ◽  
C Peptide ◽  
Hyperglycemic Clamp ◽  
History Of ◽  
Plasma Ffa

Elevated plasma FFA cause β-cell lipotoxicity and impair insulin secretion in nondiabetic subjects predisposed to type 2 diabetes mellitus [T2DM; i.e., with a strong family history of T2DM (FH+)] but not in nondiabetic subjects without a family history of T2DM. To determine whether lowering plasma FFA with acipimox, an antilipolytic nicotinic acid derivative, may enhance insulin secretion, nine FH+ volunteers were admitted twice and received in random order either acipimox or placebo (double-blind) for 48 h. Plasma glucose/insulin/C-peptide concentrations were measured from 0800 to 2400. On day 3, insulin secretion rates (ISRs) were assessed during a +125 mg/dl hyperglycemic clamp. Acipimox reduced 48-h plasma FFA by 36% ( P < 0.001) and increased the plasma C-peptide relative to the plasma glucose concentration or ΔC-peptide/Δglucose AUC (+177%, P = 0.02), an index of improved β-cell function. Acipimox improved insulin sensitivity (M/I) 26.1 ± 5% ( P < 0.04). First- (+19 ± 6%, P = 0.1) and second-phase (+31 ± 6%, P = 0.05) ISRs during the hyperglycemic clamp also improved. This was particularly evident when examined relative to the prevailing insulin resistance [1/(M/I)], as both first- and second-phase ISR markedly increased by 29 ± 7 ( P < 0.05) and 41 ± 8% ( P = 0.02). There was an inverse correlation between fasting FFA and first-phase ISR ( r2 = 0.31, P < 0.02) and acute (2–4 min) glucose-induced insulin release after acipimox ( r2 =0.52, P < 0.04). In this proof-of-concept study in FH+ individuals predisposed to T2DM, a 48-h reduction of plasma FFA improves day-long meal and glucose-stimulated insulin secretion. These results provide additional evidence for the important role that plasma FFA play regarding insulin secretion in FH+ subjects predisposed to T2DM.

Phylogenetic position and evolutionary history of the turtle and whale barnacles (Cirripedia: Balanomorpha: Coronuloidea)

2013 ◽  
Vol 67 (1) ◽  
pp. 9-14 ◽  
Author(s):  
Ryota Hayashi ◽  
Benny K.K. Chan ◽  
Noa Simon-Blecher ◽  
Hiromi Watanabe ◽  
Tamar Guy-Haim ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Position ◽  
History Of

Association of +505A>G Polymorphism at TAFI Gene with Recurrent Miscarriage in Iranian Women

2021 ◽  
Author(s):  
Razieh Alivand ◽  
Fatemeh Abdi ◽  
Mahmood Dehghani-Ashkezari ◽  
Hossein Neamatzadeh ◽  
Sedigheh Ekraminasab
Keyword(s):  
Recurrent Miscarriage ◽  
Iranian Women ◽  
Specific Pcr ◽  
Study Results ◽  
Significant Difference ◽  
Fibrinolysis Inhibitor ◽  
History Of ◽  
Allele Specific ◽  
Allele Specific Pcr ◽  
Control Study

Background: Recurrent miscarriage (RM) is one of the major problems of public health globally. The thrombin-activatable fibrinolysis inhibitor (TAFI) gene is a plasma zymogen that regulates both fibrinolysis and inflammation. Genetic variants within TAFI gene are presumed to be associated with development of RM. This case-control study aimed to investigate the association of TAFI +505A>G polymorphism with RM in Iranian women referred to Meybod Genetic Center. Methods: Fifty women with RM (at least 2 miscarriages) and 50 healthy women with no history of miscarriage or other fertility complications were participated in this study. The TAFI +505A>G polymorphism was genotyped by allele specific PCR (AS-PCR) assay. Results: The mean age of cases with RM and controls was 27.25 ± 4.31 and 28.42 ± 3.22 years, respectively. The frequency of GG genotype and G allele was 0.00% in patients and controls. There was no significant difference between RM cases and controls in terms of +505A>G genotypes and alleles. Conclusion: This study results indicated that there was no significant relationship between the TAFI +505A>G polymorphism and RM risk in Iranian women. However, further rigorous, studies with a larger sample size and different ethnicity are necessary to confirm our findings.

Notes on the generic position of Brassica deserti (Brassicaceae)

2019 ◽  
Vol 66 (1-2) ◽  
pp. 89-93
Author(s):  
Jotham Ziffer-Berger ◽  
Alexandra Keren-Keiserman ◽  
Adi Doron-Faigenboim ◽  
Klaus Mummenhoff ◽  
Oz Barazani
Keyword(s):  
Mediterranean Area ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Molecular Tools ◽  
East Mediterranean ◽  
Phylogenetic Groups ◽  
5.8S Rdna ◽  
The Core ◽  
Generic Position ◽  
History Of

Molecular tools provide new insights into phylogenetic relationships of plant species, and by relating phylogenetic groups to their geographical distribution, we can cast light upon the evolution history of plant clades. In the current study, we evaluated the phylogenetic position of the Sinai endemic Brassica deserti (Brassicaceae), later renamed as Erucastrum deserti, based on morphological data and 5.8S rDNA and ITS (Internal Transcribed Spacer) regions. Our results indicate that B. deserti belongs to an East-Mediterranean – Saharo Arabian clade and was not assigned to the core Brassica and Erucastrum clades, respectively, which evolved in the West Mediterranean area. We tentatively conclude that Brassica deserti evolved independently of core Brassica and Erucastrum.

scholarly journals Three new Cenomanian conifers from El Chango (Chiapas, Mexico) offer a snapshot of the geographic mosaic of the Mesozoic conifer decline

2021 ◽  
Author(s):  
Ixchel Gonzalez-Ramirez ◽  
Sergio RS Cevallos-Ferriz ◽  
Carl Rothfels
Keyword(s):  
Evolutionary History ◽  
Mixed Forest ◽  
Freshwater Ecosystems ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Dominant Group ◽  
Geographic Mosaic ◽  
History Of ◽  
Rare Opportunity

Premise of study: El Chango is a recently discovered quarry that contains extremely well preserved fossils. The Cenomanian age of the locality corresponds to a time when the global flora was transitioning from gymnosperm- to angiosperm-dominated, yet conifers predominate in this locality. These fossils thus provide a rare opportunity to understand the replacement of conifers by angiosperms as the dominant group of plants. Methods: We collected material from El Chango in annual expeditions (2010 to 2014). We selected the three most abundant and best preserved conifer morphotypes and conducted a total-evidence (i.e., including molecular and morphological data) phylogenetic analysis of a sample of 72 extant conifer species plus the three fossils. We use these results to inform our taxonomic decisions. Results: We obtained four equally most-parsimonious trees (consistency index = 44.1%, retention index = 78.8%). Despite ambiguous relationships among some extant taxa, the three fossil conifers had the same phylogenetic position in all four most parsimonious trees; we describe these species as new: Sequoiadendron helicalancifolium sp. nov. (Cupressaceae), and Microcachrys rhomboidea sp. nov. and Dacrydium bifoliosus sp. nov (Podocarpaceae). The ecosystem is interpreted as a coastal humid mixed forest. Conclusions: Our findings contribute to the understanding of Cenomanian equatorialregions, and support the hypothesis of a geographically and ecologically structured rise of angiosperms, with conifers remaining dominant in brackish-water and angiosperms becoming dominant in freshwater-ecosystems. These fossils fill in gaps in the evolutionary history of lineages like Microcachrys, which we demonstrate occurred in the Northern hemisphere before becoming restricted to its current range (Tasmania).

scholarly journals IODP Expedition 318: From Greenhouse to Icehouse at the Wilkes Land Antarctic Margin

2011 ◽  
Vol 12 ◽  
pp. 15-23 ◽  
Author(s):  
C. Escutia ◽  
H. Brinkhuis ◽  
A. Klaus ◽  
Keyword(s):  
Middle Eocene ◽  
Second Phase ◽  
Last Deglaciation ◽  
Ocean Drilling Program ◽  
Ocean Drilling ◽  
Integrated Ocean Drilling Program ◽  
Tectonic History ◽  
Wilkes Land ◽  
History Of

Integrated Ocean Drilling Program (IODP) Expedition 318, Wilkes Land Glacial History, drilled a transect of sites across the Wilkes Land margin of Antarctica to provide a long-term record of the sedimentary archives of Cenozoic Antarctic glaciation and its intimate relationships with global climatic and oceanographic change. The Wilkes Land drilling program was undertaken to constrain the age, nature, and paleoenvironment of the previously only seismically inferred glacial sequences. The expedition (January–March 2010) recovered ~2000 meters of high-quality middle Eocene–Holocene sediments from water depths between 400 m and 4000 m at four sites on the Wilkes Land rise (U1355, U1356, U1359, and U1361) and three sites on the Wilkes Land shelf (U1357, U1358, and U1360). <br><br> These records span ~53 million years of Antarctic history, and the various seismic units (WL-S4–WL-S9) have been successfully dated. The cores reveal the history of the Wilkes Land Antarctic margin from an ice-free “greenhouse” Antarctica, to the first cooling, to the onset and erosional consequences of the first glaciation and the subsequent dynamics of the waxing and waning ice sheets, all the way to thick, unprecedented "tree ring style" records with seasonal resolution of the last deglaciation that began ~10,000 y ago. The cores also reveal details of the tectonic history of the Australo-Antarctic Gulf from 53 Ma, portraying the onset of the second phase of rifting between Australia and Antarctica, to ever-subsiding margins and deepening, to the present continental and ever-widening ocean/continent configuration. <br><br> doi:<a href="http://dx.doi.org/10.2204/iodp.sd.12.02.2011" target="_blank">10.2204/iodp.sd.12.02.2011</a>

scholarly journals A Review of the Application of Next Generation Sequencing (NGS) in Wild Terrestrial Vertebrate Research

2019 ◽  
pp. 1-9 ◽  
Author(s):  
Ramitha Arumugam ◽  
Joey Ee Uli ◽  
Geetha Annavi
Keyword(s):  
Life Science ◽  
Review Paper ◽  
High Reliability ◽  
Next Generation ◽  
Detailed Understanding ◽  
Terrestrial Vertebrate ◽  
Look Back ◽  
History Of ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

In era of sequencing revolution, scientists seek for knowledge about the ever-expanding field of technology, Next Generation Sequence (NGS) to be applied in their research due to its high reliability and rate of discovery. What is NGS? To obtain a detailed understanding about NGS, it is required to look back the history of sequencing and how the NGS stepped into life science. This review paper gives an overview of NGS projects in wild terrestrial vertebrate including applications such as whole genome sequencing and metagenomics.

scholarly journals Coronavirus in light of philosophy

2021 ◽  
Vol 12 (1) ◽  
pp. 6-32
Author(s):  
Emil Vlajki
Keyword(s):  
Genetic Manipulation ◽  
Positive Impact ◽  
Technological Development ◽  
Modern Medicine ◽  
Human Virus ◽  
The Us ◽  
History Of ◽  
Ancient Times ◽  
The Subject ◽  
Scientific And Technological Development

The history of humanity is a history of rationality. As a result, mankind has progressed from the Stone Age to the era of modern medicine, genetics, computer science, robotics, and nanotechnology. The life span of a man in ancient times was about twenty years, and today, in highly developed societies, a man lives, on average, to eighty-six years. Advances in science and technology have not always had a positive impact. Suffice to say, the ongoing environmental problems that seriously affect humanity or, for example, the dietary problems that have resulted due to genetic manipulation. Scientific and technological development must be considered in a serious and philosophical manner. Ethics are increasingly becoming an integral part of life. In this paper, we focused on the new coronavirus that has led to the planetary-wide disease called COVID-19. All countries have engaged in their efforts to suppress the resulting pandemic. However, some of the utilized measures have been suspect: whether to lock-down people in quarantine, whether their movement should be restricted, whether they should be forced to vaccinate, and so on. Claiming to act prophylactically, scientists, by adding some DNA, RNA segments (gain of function, GOF) to an innocuous human virus, have created a dangerous artificial influenza virus. Likewise, an artificial, infectious coronavirus was created in a laboratory. Both procedures for creating these dangerous, hybrid viruses have been described in eminent scientific journals. The scientists involved in this research told us that they wanted to find cures and vaccines for these non-natural viruses on the off-chance they ever appeared among humans; when carefully handled, engineered organisms provide a unique opportunity to study biological systems in a controlled fashion. Biotechnology is a powerful tool to advance medical research and should not be abandoned because of irrational fears. But the chance of this type of virus appearing among humans is almost non-existent. However, what if these viruses "escape" from the lab, as has happened in the recent past? What if a terrorist organization start producing these viruses on their own according to detailed instructions and then use them? Finally, since the two great world powers, the US and China, that jointly created the artificial coronavirus, called SHC014-MA15, who can stop them from continuing this practice? Isn't it possible that they also created the current SARS-CoV-2 provoking a death of two and a half million people? Related to these questions, this study deals with the issue of tolerance. A large number of world-renowned scientists really believe that the current cause of the pandemic, SARS-CoV-2, is an artificial, laboratory-created virus, presenting a number of facts for this. It is not disputed that their claims are arguable. This, however, does not mean that their opponents, pharmaceutical companies and some superpowers, who have far greater political and economic power, have to incorrectly and utterly embarrass them all over, morally discredit them, nor ban their texts on the subject. In science, the struggle must be waged by arguments, not by totalitarian Orwellian methods.

scholarly journals Phylogenetic position and taxonomy of Cycloseris explanulata and C. wellsi (Scleractinia: Fungiidae): lost mushroom corals find their way home

2012 ◽  
Vol 81 (3) ◽  
pp. 125-146 ◽  
Author(s):  
Francesca Benzoni ◽  
Roberto Arrigoni ◽  
Fabrizio Stefani ◽  
Bastian T. Reijnen ◽  
Simone Montano ◽  
...  
Keyword(s):  
Molecular Study ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Distribution Data ◽  
Data Sets ◽  
Free Living ◽  
New Findings ◽  
The Family ◽  
Ecological Implications ◽  
History Of

The scleractinian species Psammocora explanulata and Coscinaraea wellsi were originally classified in the family Siderastreidae, but in a recent morpho-molecular study it appeared that they are more closely related to each other and to the Fungiidae than to any siderastreid taxon. A subsequent morpho-molecular study of the Fungiidae provided new insights regarding the phylogenetic relationships within that family. In the present study existing molecular data sets of both families were analyzed jointly with those of new specimens and sequences of P. explanulata and C. wellsi. The results indicate that both species actually belong to the Cycloseris clade within the family Fungiidae. A reappraisal of their morphologic characters based on museum specimens and recently collected material substantiate the molecular results. Consequently, they are renamed Cycloseris explanulata and C. wellsi. They are polystomatous and encrusting like C. mokai, another species recently added to the genus, whereas all Cycloseris species were initially thought to be monostomatous and free-living. In the light of the new findings, the taxonomy and distribution data of C. explanulata and C. wellsi have been updated and revised. Finally, the ecological implications of the evolutionary history of the three encrusting polystomatous Cycloseris species and their free-living monostomatous congeners are discussed.

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